@cyanheads/brapi-mcp-server 0.7.10 → 0.7.12

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (121) hide show
  1. package/CLAUDE.md +32 -25
  2. package/Dockerfile +19 -5
  3. package/README.md +7 -4
  4. package/changelog/0.7.x/0.7.11.md +43 -0
  5. package/changelog/0.7.x/0.7.12.md +35 -0
  6. package/changelog/template.md +62 -40
  7. package/dist/config/alias-credentials.d.ts +1 -1
  8. package/dist/config/alias-credentials.d.ts.map +1 -1
  9. package/dist/config/alias-credentials.js +24 -8
  10. package/dist/config/alias-credentials.js.map +1 -1
  11. package/dist/config/builtin-aliases.js.map +1 -1
  12. package/dist/config/server-config.d.ts +1 -1
  13. package/dist/config/server-config.d.ts.map +1 -1
  14. package/dist/config/server-config.js +3 -1
  15. package/dist/config/server-config.js.map +1 -1
  16. package/dist/mcp-server/resources/definitions/brapi-calls.resource.d.ts +3 -3
  17. package/dist/mcp-server/resources/definitions/brapi-calls.resource.d.ts.map +1 -1
  18. package/dist/mcp-server/resources/definitions/brapi-calls.resource.js +1 -1
  19. package/dist/mcp-server/resources/definitions/brapi-filters.resource.d.ts +3 -3
  20. package/dist/mcp-server/resources/definitions/brapi-filters.resource.d.ts.map +1 -1
  21. package/dist/mcp-server/resources/definitions/brapi-filters.resource.js +1 -1
  22. package/dist/mcp-server/resources/definitions/brapi-germplasm.resource.d.ts +6 -6
  23. package/dist/mcp-server/resources/definitions/brapi-germplasm.resource.d.ts.map +1 -1
  24. package/dist/mcp-server/resources/definitions/brapi-germplasm.resource.js +1 -1
  25. package/dist/mcp-server/resources/definitions/brapi-server-info.resource.d.ts +3 -3
  26. package/dist/mcp-server/resources/definitions/brapi-server-info.resource.d.ts.map +1 -1
  27. package/dist/mcp-server/resources/definitions/brapi-server-info.resource.js +1 -1
  28. package/dist/mcp-server/resources/definitions/brapi-study.resource.d.ts +6 -6
  29. package/dist/mcp-server/resources/definitions/brapi-study.resource.d.ts.map +1 -1
  30. package/dist/mcp-server/resources/definitions/brapi-study.resource.js +1 -1
  31. package/dist/mcp-server/resources/definitions/brapi-variable.resource.d.ts +6 -6
  32. package/dist/mcp-server/resources/definitions/brapi-variable.resource.d.ts.map +1 -1
  33. package/dist/mcp-server/resources/definitions/brapi-variable.resource.js +1 -1
  34. package/dist/mcp-server/tools/definitions/brapi-build-phenotype-matrix.tool.d.ts +19 -14
  35. package/dist/mcp-server/tools/definitions/brapi-build-phenotype-matrix.tool.d.ts.map +1 -1
  36. package/dist/mcp-server/tools/definitions/brapi-build-phenotype-matrix.tool.js +34 -0
  37. package/dist/mcp-server/tools/definitions/brapi-build-phenotype-matrix.tool.js.map +1 -1
  38. package/dist/mcp-server/tools/definitions/brapi-connect.tool.d.ts +12 -12
  39. package/dist/mcp-server/tools/definitions/brapi-connect.tool.d.ts.map +1 -1
  40. package/dist/mcp-server/tools/definitions/brapi-dataframe-describe.tool.d.ts +2 -2
  41. package/dist/mcp-server/tools/definitions/brapi-dataframe-describe.tool.d.ts.map +1 -1
  42. package/dist/mcp-server/tools/definitions/brapi-dataframe-export.tool.d.ts +14 -14
  43. package/dist/mcp-server/tools/definitions/brapi-dataframe-export.tool.d.ts.map +1 -1
  44. package/dist/mcp-server/tools/definitions/brapi-dataframe-query.tool.d.ts +9 -4
  45. package/dist/mcp-server/tools/definitions/brapi-dataframe-query.tool.d.ts.map +1 -1
  46. package/dist/mcp-server/tools/definitions/brapi-dataframe-query.tool.js +31 -0
  47. package/dist/mcp-server/tools/definitions/brapi-dataframe-query.tool.js.map +1 -1
  48. package/dist/mcp-server/tools/definitions/brapi-describe-filters.tool.d.ts +6 -6
  49. package/dist/mcp-server/tools/definitions/brapi-describe-filters.tool.d.ts.map +1 -1
  50. package/dist/mcp-server/tools/definitions/brapi-export-genotype-matrix.tool.d.ts +11 -11
  51. package/dist/mcp-server/tools/definitions/brapi-export-genotype-matrix.tool.d.ts.map +1 -1
  52. package/dist/mcp-server/tools/definitions/brapi-find-genotype-calls.tool.d.ts +11 -11
  53. package/dist/mcp-server/tools/definitions/brapi-find-genotype-calls.tool.d.ts.map +1 -1
  54. package/dist/mcp-server/tools/definitions/brapi-find-germplasm.tool.d.ts +6 -6
  55. package/dist/mcp-server/tools/definitions/brapi-find-germplasm.tool.d.ts.map +1 -1
  56. package/dist/mcp-server/tools/definitions/brapi-find-images.tool.d.ts +6 -6
  57. package/dist/mcp-server/tools/definitions/brapi-find-images.tool.d.ts.map +1 -1
  58. package/dist/mcp-server/tools/definitions/brapi-find-locations.tool.d.ts +6 -6
  59. package/dist/mcp-server/tools/definitions/brapi-find-locations.tool.d.ts.map +1 -1
  60. package/dist/mcp-server/tools/definitions/brapi-find-observations.tool.d.ts +6 -6
  61. package/dist/mcp-server/tools/definitions/brapi-find-observations.tool.d.ts.map +1 -1
  62. package/dist/mcp-server/tools/definitions/brapi-find-studies.tool.d.ts +6 -6
  63. package/dist/mcp-server/tools/definitions/brapi-find-studies.tool.d.ts.map +1 -1
  64. package/dist/mcp-server/tools/definitions/brapi-find-variables.tool.d.ts +7 -7
  65. package/dist/mcp-server/tools/definitions/brapi-find-variables.tool.d.ts.map +1 -1
  66. package/dist/mcp-server/tools/definitions/brapi-find-variants.tool.d.ts +6 -6
  67. package/dist/mcp-server/tools/definitions/brapi-find-variants.tool.d.ts.map +1 -1
  68. package/dist/mcp-server/tools/definitions/brapi-germplasm-performance.tool.d.ts +6 -6
  69. package/dist/mcp-server/tools/definitions/brapi-germplasm-performance.tool.d.ts.map +1 -1
  70. package/dist/mcp-server/tools/definitions/brapi-get-germplasm.tool.d.ts +6 -6
  71. package/dist/mcp-server/tools/definitions/brapi-get-germplasm.tool.d.ts.map +1 -1
  72. package/dist/mcp-server/tools/definitions/brapi-get-image.tool.d.ts +6 -6
  73. package/dist/mcp-server/tools/definitions/brapi-get-image.tool.d.ts.map +1 -1
  74. package/dist/mcp-server/tools/definitions/brapi-get-study.tool.d.ts +6 -6
  75. package/dist/mcp-server/tools/definitions/brapi-get-study.tool.d.ts.map +1 -1
  76. package/dist/mcp-server/tools/definitions/brapi-raw-get.tool.d.ts +6 -6
  77. package/dist/mcp-server/tools/definitions/brapi-raw-get.tool.d.ts.map +1 -1
  78. package/dist/mcp-server/tools/definitions/brapi-raw-search.tool.d.ts +7 -7
  79. package/dist/mcp-server/tools/definitions/brapi-raw-search.tool.d.ts.map +1 -1
  80. package/dist/mcp-server/tools/definitions/brapi-server-info.tool.d.ts +9 -9
  81. package/dist/mcp-server/tools/definitions/brapi-server-info.tool.d.ts.map +1 -1
  82. package/dist/mcp-server/tools/definitions/brapi-submit-observations.tool.d.ts +23 -27
  83. package/dist/mcp-server/tools/definitions/brapi-submit-observations.tool.d.ts.map +1 -1
  84. package/dist/mcp-server/tools/definitions/brapi-submit-observations.tool.js +41 -55
  85. package/dist/mcp-server/tools/definitions/brapi-submit-observations.tool.js.map +1 -1
  86. package/dist/mcp-server/tools/definitions/brapi-walk-pedigree.tool.d.ts +8 -8
  87. package/dist/mcp-server/tools/definitions/brapi-walk-pedigree.tool.d.ts.map +1 -1
  88. package/dist/mcp-server/tools/definitions/index.d.ts +829 -824
  89. package/dist/mcp-server/tools/definitions/index.d.ts.map +1 -1
  90. package/dist/mcp-server/tools/shared/find-helpers.js.map +1 -1
  91. package/dist/mcp-server/tools/shared/observations.js.map +1 -1
  92. package/dist/mcp-server/tools/shared/orientation-envelope.d.ts +12 -12
  93. package/dist/services/brapi-client/brapi-client.d.ts +2 -3
  94. package/dist/services/brapi-client/brapi-client.d.ts.map +1 -1
  95. package/dist/services/brapi-client/brapi-client.js +16 -19
  96. package/dist/services/brapi-client/brapi-client.js.map +1 -1
  97. package/dist/services/brapi-client/types.d.ts +2 -2
  98. package/dist/services/brapi-dialect/detect.d.ts +1 -1
  99. package/dist/services/brapi-dialect/detect.js.map +1 -1
  100. package/dist/services/brapi-dialect/index.d.ts +2 -2
  101. package/dist/services/brapi-dialect/index.js +1 -1
  102. package/dist/services/brapi-dialect/index.js.map +1 -1
  103. package/dist/services/canvas-bridge/canvas-bridge.d.ts +1 -1
  104. package/dist/services/canvas-bridge/canvas-bridge.d.ts.map +1 -1
  105. package/dist/services/canvas-bridge/canvas-bridge.js.map +1 -1
  106. package/dist/services/capability-registry/capability-registry.d.ts +1 -1
  107. package/dist/services/capability-registry/capability-registry.d.ts.map +1 -1
  108. package/dist/services/capability-registry/capability-registry.js +1 -1
  109. package/dist/services/capability-registry/capability-registry.js.map +1 -1
  110. package/dist/services/ontology-resolver/ontology-resolver.d.ts.map +1 -1
  111. package/dist/services/ontology-resolver/ontology-resolver.js.map +1 -1
  112. package/dist/services/reference-data-cache/reference-data-cache.d.ts +2 -2
  113. package/dist/services/reference-data-cache/reference-data-cache.d.ts.map +1 -1
  114. package/dist/services/reference-data-cache/reference-data-cache.js +1 -1
  115. package/dist/services/reference-data-cache/reference-data-cache.js.map +1 -1
  116. package/dist/services/server-registry/server-registry.d.ts.map +1 -1
  117. package/dist/services/server-registry/server-registry.js.map +1 -1
  118. package/dist/services/server-registry/types.d.ts +1 -1
  119. package/manifest.json +8 -6
  120. package/package.json +15 -14
  121. package/server.json +3 -3
@@ -13,8 +13,8 @@ import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
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  export declare const brapiWalkPedigree: import("@cyanheads/mcp-ts-core").ToolDefinition<z.ZodObject<{
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  germplasmDbIds: z.ZodArray<z.ZodString>;
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  direction: z.ZodDefault<z.ZodEnum<{
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- both: "both";
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  ancestors: "ancestors";
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+ both: "both";
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  descendants: "descendants";
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  }>>;
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  maxDepth: z.ZodDefault<z.ZodNumber>;
@@ -23,8 +23,8 @@ export declare const brapiWalkPedigree: import("@cyanheads/mcp-ts-core").ToolDef
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  }, z.core.$strip>, z.ZodObject<{
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  alias: z.ZodString;
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  direction: z.ZodEnum<{
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- both: "both";
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  ancestors: "ancestors";
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+ both: "both";
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  descendants: "descendants";
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  }>;
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  maxDepth: z.ZodNumber;
@@ -34,18 +34,18 @@ export declare const brapiWalkPedigree: import("@cyanheads/mcp-ts-core").ToolDef
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  depth: z.ZodNumber;
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  isRoot: z.ZodBoolean;
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  direction: z.ZodEnum<{
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- root: "root";
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  ancestor: "ancestor";
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- descendant: "descendant";
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  both: "both";
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+ descendant: "descendant";
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+ root: "root";
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  }>;
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  }, z.core.$strip>>;
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  edges: z.ZodArray<z.ZodObject<{
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  from: z.ZodString;
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  to: z.ZodString;
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  relationship: z.ZodEnum<{
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- parent: "parent";
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  child: "child";
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+ parent: "parent";
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  }>;
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  parentType: z.ZodOptional<z.ZodString>;
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  }, z.core.$strip>>;
@@ -79,9 +79,9 @@ export declare const brapiWalkPedigree: import("@cyanheads/mcp-ts-core").ToolDef
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  totalCount: z.ZodOptional<z.ZodNumber>;
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  }, z.core.$strip>>;
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  }, z.core.$strip>, readonly [{
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- readonly reason: "unknown_alias";
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+ readonly reason: 'unknown_alias';
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  readonly code: JsonRpcErrorCode.NotFound;
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- readonly when: "No connection has been registered under the requested alias";
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- readonly recovery: "Run brapi_connect with this alias (or omit `alias` to use the default connection) before calling brapi_walk_pedigree.";
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+ readonly when: 'No connection has been registered under the requested alias';
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+ readonly recovery: 'Run brapi_connect with this alias (or omit `alias` to use the default connection) before calling brapi_walk_pedigree.';
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  }], undefined>;
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  //# sourceMappingURL=brapi-walk-pedigree.tool.d.ts.map
@@ -1 +1 @@
1
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1
+ {"version":3,"file":"brapi-walk-pedigree.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-walk-pedigree.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;;GASG;AAEH,OAAO,EAAsB,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAC/D,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAgHjE,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;qBAMhB,eAAe;;mBAEjB,6DAA6D;uBAEjE,uHAAuH;cA0S7H,CAAC"}